2RVH | pdb_00002rvh

NMR structure of eIF1

• PDB DOI: https://doi.org/10.2210/pdb2RVH/pdb
• BMRB: 11599

• Classification: TRANSLATION
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-10-16 Released: 2016-10-26 
• Deposition Author(s): Nagata, T., Obayashi, E., Asano, K.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Molecular Landscape of the Ribosome Pre-initiation Complex during mRNA Scanning: Structural Role for eIF3c and Its Control by eIF5

Obayashi, E., Luna, R.E., Nagata, T., Martin-Marcos, P., Hiraishi, H., Singh, C.R., Erzberger, J.P., Zhang, F., Arthanari, H., Morris, J., Pellarin, R., Moore, C., Harmon, I., Papadopoulos, E., Yoshida, H., Nasr, M.L., Unzai, S., Thompson, B., Aube, E., Hustak, S., Stengel, F., Dagraca, E., Ananbandam, A., Gao, P., Urano, T., Hinnebusch, A.G., Wagner, G., Asano, K.

(2017) Cell Rep 18: 2651-2663

• PubMed: 28297669 
• DOI: https://doi.org/10.1016/j.celrep.2017.02.052
• Primary Citation Related Structures: 
  2RVH, 5H7U


• PubMed Abstract: 
  

  During eukaryotic translation initiation, eIF3 binds the solvent-accessible side of the 40S ribosome and recruits the gate-keeper protein eIF1 and eIF5 to the decoding center. This is largely mediated by the N-terminal domain (NTD) of eIF3c, which can be divided into three parts: 3c0, 3c1, and 3c2. The N-terminal part, 3c0, binds eIF5 strongly but only weakly to the ribosome-binding surface of eIF1, whereas 3c1 and 3c2 form a stoichiometric complex with eIF1. 3c1 contacts eIF1 through Arg-53 and Leu-96, while 3c2 faces 40S protein uS15/S13, to anchor eIF1 to the scanning pre-initiation complex (PIC). We propose that the 3c0:eIF1 interaction diminishes eIF1 binding to the 40S, whereas 3c0:eIF5 interaction stabilizes the scanning PIC by precluding this inhibitory interaction. Upon start codon recognition, interactions involving eIF5, and ultimately 3c0:eIF1 association, facilitate eIF1 release. Our results reveal intricate molecular interactions within the PIC, programmed for rapid scanning-arrest at the start codon.

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Organizational Affiliation: 
• Shimane University School of Medicine, Izumo, Shimane 690-8504, Japan.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA.
Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.
California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA.
Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama 230-0045, Japan; Drug Design Group, Kanagawa Academy of Science and Technology, Takatsu-ku, Kawasaki 213-0012, Japan.
Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama 230-0045, Japan.
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.
COBRE-PSF, University of Kansas, Lawrence, KS 66047, USA.
Molecular Cellular Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 12.33 kDa 
• Atom Count: 863 
• Modeled Residue Count: 108 
• Deposited Residue Count: 108 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor eIF-1	A	108	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SUI1, RFR1, YNL244C, N0905
UniProt
Find proteins for P32911 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32911  Go to UniProtKB:  P32911

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-26 
Deposition Author(s): Nagata, T., Obayashi, E., Asano, K.

Revision History  

• Version 1.0: 2016-10-26
  Type: Initial release
  
• Version 1.1: 2017-05-31
  Changes: Database references
• Version 1.2: 2023-06-14
  Changes: Data collection, Database references, Other
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references